rs149225

Positions:

• chr4-154762064-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515071.1(ENSG00000249041):​n.300-1023A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,116 control chromosomes in the GnomAD database, including 29,171 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (29171 hom., cov: 32)
• Consequence: ENSG00000249041 ENST00000515071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

Genes affected

ENSG00000249041 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377500	NR_188451.1	n.300-1023A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249041	ENST00000515071.1	n.300-1023A>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88932 AN: 151998 Hom.: 29127 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.554

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.585 AC: 89042 AN: 152116 Hom.: 29171 Cov.: 32 AF XY: 0.593 AC XY: 44113 AN XY: 74338

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.555

Alfa AF: 0.522 Hom.: 2977

Bravo AF: 0.609

Asia WGS AF: 0.675 AC: 2348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs149225; hg19: chr4-155683216;